When comparing WinSCP vs SSH of Windows' Linux subsystem, the Slant community recommends SSH of Windows' Linux subsystem for most people. In the question“What are the best SSH clients for Windows?” SSH of Windows' Linux subsystem is ranked 5th while WinSCP is ranked 17th. The most important reason people chose SSH of Windows' Linux subsystem is:
All you have to do is go to the Microsoft store, choose a Linux distro you like, and install the client for free.
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Pros
Pro Supports FTP and SFTP
In new versions also supports WebDav.
Pro Free and open-source
It has very good compatibility with the other tools of this segment (e.g. PuTTY).
Pro Supports WebDAV
Pro Not bundled with Potentially Unwanted Programs (PUP)
Does not attempt to install unwanted software on installation.
Pro Supports PPK Keys
You can use the SSH server public/private key files from putty to log in.
Pro Supports Amazon S3
You can use in the last versions S3 so you're good if you use Amazon AWS.
Pro Portable
No Installation required.
Pro Integrated basic text editor
It has a integrated basic function text editor to create/edit/update files directly from client.
Pro Can protect stored passwords by strong AES cipher
Pro Can be automated with batch scripts
Put a line in bat file ""D:\Program Files\WinSCP\winscp.com" /console /script="D:\ftp\scripts\transfer.txt". All the info can be found on their site.
Pro It's extremely easy to get running
All you have to do is go to the Microsoft store, choose a Linux distro you like, and install the client for free.
Pro Based on OpenSSH
OpenSSH is the reference for all ssh clients.
Pro Excellent way for Windows users to learn Linux
It is much easier and more convenient than dealing with a dual boot Linux installation.
Pro Full Linux shell
Uses all relevant Linux ssh commands as normal.
Cons
Con Keyboard shortcuts not editable
Con Slow
In my opinion, it's slower than Filezilla.
Con No x64 version
Con Does not support UNC
Does not support UNC. This makes working with the "Library"-function in Win 7, 8, 10 not possible when working over a network.
Con Weird keyboard selection handling
If you are accustomed to several commanders, the selection method in WinSCP behaves unexpected - most often selects too much.
Con Graphical problems
For example running Midnight commander (MC) makes terminal blinking.
Con Crontab and other background jobs don't work properly
Crontab only runs on ROOT, and it needs Windows to stay open. If you close it, you will kill the crontab. Some background jobs don't run on Windows WSL.
Con Command line editing does not work properly
Overrides chars instead of inserting them... depending on position and moon phase?
Con Does not install on PC virtual machines
Con Forces window to a certain size
Any other SSH client will render the remote server at whatever size the local client window is. The built-in SSH client on Windows, however, forces you to use a standard size, and it's small enough to cause problems.
Con Windows' SSH key agent service is broken
Attempting to use the built-in ssh-agent provided with Windows will cause errors and authentication failures due to an incompatibility between Windows' ssh-agent and OpenSSH on remote systems.
Con Cut & paste works like the Windows prompt
Older versions of the Windows Command Prompt select text in a rectangular region of the console, rather than starting at a character position and selecting forward or backward along with the logical flow of text. To copy a sentence, for example, would require that you select all content in the two lines that contain the sentence, then trim what isn't needed, rather than just selecting the sentence. In later versions of Windows 10, this may not be an issue, as the cut-and-paste behavior has changed.
